Locus 6758

Sequence ID	2L_DroMel_CAF1
Location	18,890,652 – 18,890,744
Length	92
Max. P	0.995420

overview

Window 2

Location	18,890,652 – 18,890,744
Length	92
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	77.11
Mean single sequence MFE	-22.95
Consensus MFE	-13.22
Energy contribution	-14.02
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-2.66
Structure conservation index	0.58
SVM decision value	2.57
SVM RNA-class probability	0.995420
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18890652 92 + 22407834
CCAUAAAUCAUAAAGACGCGACCUCGGAUCGGUGUCCCC-----AGCCAUACA----CUCGCACAUAUAUCCA-----------ACUCCAUGGACACCGAUCUCGUCUCCGA
.............(((((((....))(((((((((((..-----.........----................-----------.......))))))))))).))))).... ( -23.28)
>DroSec_CAF1 16037 103 + 1
CCAUAAAUCAUAAAGACGCGACCUCCGAUCGGUGUCCCC-----AGCCAUACA----CUCGAACAUAUACCCAUAUGUACAUAUACUCCAGGGACUCCGAUCUCGUCUCCGA
..............((.((((.....((((((.(((((.-----.(.....).----...(.((((((....)))))).)..........))))).)))))))))).))... ( -24.80)
>DroSim_CAF1 14319 80 + 1
CCAUAAAUCAUAAAGCCGCGACCUCCGAUCGGUGUCCCC-----AGCCAUUUA----C------------CCA-----------ACUCCAUGGACUCCGAUCUCGUCUCCGA
................((.(((....((((((.((((..-----.........----.------------...-----------.......)))).))))))..)))..)). ( -16.75)
>DroEre_CAF1 13837 95 + 1
CCAUAAAUCAUAAAGACGCGACCUCG-AUCGGUGGCCCC-----AGCCAAAUACGCGUACCUACAUAUACCAA-----------UCUCCAUGGACUCCGAUCUCGUCUCCGA
.............(((((.(....)(-(((((((((...-----.))))....................(((.-----------......)))...)))))).))))).... ( -18.70)
>DroYak_CAF1 14120 99 + 1
CCAUAAAUCAUAAAGACGCGACCUCGGAUCGGAGGCCCUUAUGGAGUCAUAU--GGACUCGUGCAUAUACAAA-----------UCUCCAUGGACUCCGAUCUCGUCUCCGA
.............(((((((....))((((((((..((..((((((..((((--(.(....).))))).....-----------.)))))))).)))))))).))))).... ( -31.20)
>consensus
CCAUAAAUCAUAAAGACGCGACCUCGGAUCGGUGUCCCC_____AGCCAUAUA____CUCGUACAUAUACCCA___________ACUCCAUGGACUCCGAUCUCGUCUCCGA
..............((.((((.....((((((.((((......................................................)))).)))))))))).))... (-13.22 = -14.02 +   0.80)

alignment

secondary structure

dotplot

Window 3

Location	18,890,652 – 18,890,744
Length	92
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	77.11
Mean single sequence MFE	-33.14
Consensus MFE	-16.92
Energy contribution	-17.52
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.42
Structure conservation index	0.51
SVM decision value	1.83
SVM RNA-class probability	0.979089
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18890652 92 - 22407834
UCGGAGACGAGAUCGGUGUCCAUGGAGU-----------UGGAUAUAUGUGCGAG----UGUAUGGCU-----GGGGACACCGAUCCGAGGUCGCGUCUUUAUGAUUUAUGG
..(((((((.(((((((((((....(((-----------(..((((((......)----)))))))))-----..)))))))))))((....)))))))))........... ( -32.80)
>DroSec_CAF1 16037 103 - 1
UCGGAGACGAGAUCGGAGUCCCUGGAGUAUAUGUACAUAUGGGUAUAUGUUCGAG----UGUAUGGCU-----GGGGACACCGAUCGGAGGUCGCGUCUUUAUGAUUUAUGG
..(((((((.((((((.(((((..(.((((((..((((((....))))))....)----)))))..).-----.))))).))))))........)))))))........... ( -39.90)
>DroSim_CAF1 14319 80 - 1
UCGGAGACGAGAUCGGAGUCCAUGGAGU-----------UGG------------G----UAAAUGGCU-----GGGGACACCGAUCGGAGGUCGCGGCUUUAUGAUUUAUGG
(((....)))((((((.((((..((.((-----------(..------------.----..)))..))-----..)))).)))))).(((((....)))))........... ( -26.80)
>DroEre_CAF1 13837 95 - 1
UCGGAGACGAGAUCGGAGUCCAUGGAGA-----------UUGGUAUAUGUAGGUACGCGUAUUUGGCU-----GGGGCCACCGAU-CGAGGUCGCGUCUUUAUGAUUUAUGG
..(((((((.((((....((....))((-----------(((((((((((......))))))..(((.-----...)))))))))-)..)))).)))))))........... ( -30.80)
>DroYak_CAF1 14120 99 - 1
UCGGAGACGAGAUCGGAGUCCAUGGAGA-----------UUUGUAUAUGCACGAGUCC--AUAUGACUCCAUAAGGGCCUCCGAUCCGAGGUCGCGUCUUUAUGAUUUAUGG
..(((((((.....((((((.(((..((-----------(((((......))))))).--.))))))))).....((((((......)))))).)))))))........... ( -35.40)
>consensus
UCGGAGACGAGAUCGGAGUCCAUGGAGU___________UGGGUAUAUGUACGAG____UAUAUGGCU_____GGGGACACCGAUCCGAGGUCGCGUCUUUAUGAUUUAUGG
(((....)))((((((.((((......................................................)))).))))))..((((((........)))))).... (-16.92 = -17.52 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:19:18 2006